Re: [ccp4bb] Software to Produce Linear Map of Surface Accessible Residues
On 11/02/2010 02:36 PM, Buz Barstow wrote: Dear All, I'm looking for a software program to produce, given a 3D atomic structure of a molecule, a linear map showing the surface accessibility of residues in a protein structure. Would any one know of a program that can produce this sort of map. Thanks! and all the best, --Buz Have you looked at the PISA output - that lists all such information residue by residue? Eleanor
Re: [ccp4bb] Software to Produce Linear Map of Surface Accessible Residues
Dear All, Thanks for your suggestions! I ended up using the areaimol program in ccp4. My next question: Given a list of accessible surface area, is there a generally accepted value of ASA above which a residue classifies as a surface residue, while below this number it is an interior residue? Thanks! and all the best, --Buz On Nov 2, 2010, at 10:56 AM, Tim Gruene wrote: Hello Buz, I do not know what you mean by 'linear map', but according to its manual, the ccp4-program surface writes a list of accessible are per atom per residue, which you could convert into the total fraction per residue with not too much effort. Is this what you are looking for? Cheers, Tim On Tue, Nov 02, 2010 at 10:36:56AM -0400, Buz Barstow wrote: Dear All, I'm looking for a software program to produce, given a 3D atomic structure of a molecule, a linear map showing the surface accessibility of residues in a protein structure. Would any one know of a program that can produce this sort of map. Thanks! and all the best, --Buz -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A
Re: [ccp4bb] Software to Produce Linear Map of Surface Accessible Residues
That depends on what you are trying to do. Maybe the best strategy is to use fuzzy logic, whereby a residue which has 30% of it's Gly-X-Gly ASA buried has the surfaceness of 0.7. On Wed, 2010-11-03 at 09:55 -0400, Buz Barstow wrote: Dear All, Thanks for your suggestions! I ended up using the areaimol program in ccp4. My next question: Given a list of accessible surface area, is there a generally accepted value of ASA above which a residue classifies as a surface residue, while below this number it is an interior residue? Thanks! and all the best, --Buz On Nov 2, 2010, at 10:56 AM, Tim Gruene wrote: Hello Buz, I do not know what you mean by 'linear map', but according to its manual, the ccp4-program surface writes a list of accessible are per atom per residue, which you could convert into the total fraction per residue with not too much effort. Is this what you are looking for? Cheers, Tim On Tue, Nov 02, 2010 at 10:36:56AM -0400, Buz Barstow wrote: Dear All, I'm looking for a software program to produce, given a 3D atomic structure of a molecule, a linear map showing the surface accessibility of residues in a protein structure. Would any one know of a program that can produce this sort of map. Thanks! and all the best, --Buz -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore -- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. -- / Lao Tse /
Re: [ccp4bb] Software to Produce Linear Map of Surface Accessible Residues
Hi Buz, Sorry to respond a little late, but if you are still tinkering with surface accessibility calculations, you can use the following web server that will calculate the diffusion accessibility of each atom in your input .pdb file: http://nihserver.mbi.ucla.edu/diff_acc/ Diffusion accessibility is slightly different from surface accessibility, so depending on what you're interested in this may not be exactly what you want. From the web server: Diffusion accessibility gives a measure of surface accessibility that is longer range in nature than ordinary solvent accessibility. The idea of diffusion accessibility was introduced several years ago (Yeates, TO (1995) Algorithms for Evaluating the Long-range Accessibility of Protein Surfaces. J Mol Biol 249(4): 804-15). Diffusion accessibility is a measure of how easily or frequently a specific point on a surface would capture a hypothetical diffusing (or randomly-walking) probe that is captured upon its first encounter with any part of a surface. Naturally, parts of a surface that are solvent-exposed in the traditional sense but lie in a deep surface depression will capture the probe only rarely, since the probe will more often encounter another part of the surface first. The results of a diffusion accessibility calculation can be useful in quantitatively evaluating potential binding regions of a protein surface, and are particularly useful in visualization. The reason I still mention this is because diffusion accessibility vs. surface accessibility may be one way to answer your question of how to identify a surface residue vs. an interior residue. Also, the web server will output another .pdb file with the diffusion accessibility for each atom rewritten into the B-factor column. This is particularly useful for visualizing the surfaceness (as Ed put it) of each atom because you can open the output coordinates in PyMol and color atoms by B-factor which will give you a nice, colorful representation of the accessibility of the surface. Hope this is helpful, Mike - Original Message - From: Buz Barstow b...@mac.com To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, November 3, 2010 6:55:54 AM GMT -08:00 US/Canada Pacific Subject: Re: [ccp4bb] Software to Produce Linear Map of Surface Accessible Residues Dear All, Thanks for your suggestions! I ended up using the areaimol program in ccp4. My next question: Given a list of accessible surface area, is there a generally accepted value of ASA above which a residue classifies as a surface residue, while below this number it is an interior residue? Thanks! and all the best, --Buz On Nov 2, 2010, at 10:56 AM, Tim Gruene wrote: Hello Buz, I do not know what you mean by 'linear map', but according to its manual, the ccp4-program surface writes a list of accessible are per atom per residue, which you could convert into the total fraction per residue with not too much effort. Is this what you are looking for? Cheers, Tim On Tue, Nov 02, 2010 at 10:36:56AM -0400, Buz Barstow wrote: Dear All, I'm looking for a software program to produce, given a 3D atomic structure of a molecule, a linear map showing the surface accessibility of residues in a protein structure. Would any one know of a program that can produce this sort of map. Thanks! and all the best, --Buz -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A -- Michael C. Thompson Graduate Student Biochemistry Molecular Biology Division Department of Chemistry Biochemistry University of California, Los Angeles mi...@chem.ucla.edu
[ccp4bb] Software to Produce Linear Map of Surface Accessible Residues
Dear All, I'm looking for a software program to produce, given a 3D atomic structure of a molecule, a linear map showing the surface accessibility of residues in a protein structure. Would any one know of a program that can produce this sort of map. Thanks! and all the best, --Buz
Re: [ccp4bb] Software to Produce Linear Map of Surface Accessible Residues
Hello Buz, I do not know what you mean by 'linear map', but according to its manual, the ccp4-program surface writes a list of accessible are per atom per residue, which you could convert into the total fraction per residue with not too much effort. Is this what you are looking for? Cheers, Tim On Tue, Nov 02, 2010 at 10:36:56AM -0400, Buz Barstow wrote: Dear All, I'm looking for a software program to produce, given a 3D atomic structure of a molecule, a linear map showing the surface accessibility of residues in a protein structure. Would any one know of a program that can produce this sort of map. Thanks! and all the best, --Buz -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A signature.asc Description: Digital signature
Re: [ccp4bb] Software to Produce Linear Map of Surface Accessible Residues
Hi, As far as I know, thanks to Ian, areaimol in its latest versions now has an option of showing the fraction of accessible area per residue (relative to its accessible surface in the Gly-X-Gly peptide) both in the log file and in the B-factor column of the pdb file it prodcues. Cheers, Boaz - Original Message - From: Tim Gruene t...@shelx.uni-ac.gwdg.de Date: Tuesday, November 2, 2010 16:59 Subject: Re: [ccp4bb] Software to Produce Linear Map of Surface Accessible Residues To: CCP4BB@JISCMAIL.AC.UK Hello Buz, I do not know what you mean by 'linear map', but according to its manual, the ccp4-program surface writes a list of accessible are per atom per residue, which you could convert into the total fraction per residue with not too much effort. Is this what you are looking for? Cheers, Tim On Tue, Nov 02, 2010 at 10:36:56AM -0400, Buz Barstow wrote: Dear All, I'm looking for a software program to produce, given a 3D atomic structure of a molecule, a linear map showing the surface accessibility of residues in a protein structure. Would any one know of a program that can produce this sort of map. Thanks! and all the best, --Buz -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan
Re: [ccp4bb] Software to Produce Linear Map of Surface Accessible Residues
Hi, You first need a program to calculate ASA, e.g. Naccess. Once you have the ASA on a per-residue basis, you can plot a histogram, by e.g. feeding the data to a spreadsheet application of your choice. What is usually done is to list residues sequencewise vs. ASA. Best success, Nadir -- Pr. Nadir T. Mrabet Structural Molecular Biochemistry INSERM U-954 UHP - Nancy 1, School of Medicine 54505 Vandoeuvre-les-Nancy Cedex France Tel : +33 (0)3.83.68.32.73 Fax : +33 (0)3.83.68.32.79 E-mail : nadir.mra...@medecine.uhp-nancy.fr Selon Buz Barstow b...@mac.com: Dear All, I'm looking for a software program to produce, given a 3D atomic structure of a molecule, a linear map showing the surface accessibility of residues in a protein structure. Would any one know of a program that can produce this sort of map. Thanks! and all the best, --Buz
Re: [ccp4bb] Software to Produce Linear Map of Surface Accessible Residues
Try RasMol 2.7.5, e.g. load ../data/pdb1w0k.ent restrict not hoh map generate LRsurf dots map select atom within 1.8 show selected = Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 y...@dowling.edu = On Tue, 2 Nov 2010, Buz Barstow wrote: Dear All, I'm looking for a software program to produce, given a 3D atomic structure of a molecule, a linear map showing the surface accessibility of residues in a protein structure. Would any one know of a program that can produce this sort of map. Thanks! and all the best, --Buz
